1W85

The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

wwPDB Validation 3D Report Full Report



Literature

A molecular switch and proton wire synchronize the active sites in thiamine enzymes.

Frank, R.A.Titman, C.M.Pratap, J.V.Luisi, B.F.Perham, R.N.

(2004) Science 306: 872-876

  • DOI: 10.1126/science.1101030
  • Primary Citation of Related Structures:  
    1W88, 1W85

  • PubMed Abstract: 
  • Thiamine diphosphate (ThDP) is used as a cofactor in many key metabolic enzymes. We present evidence that the ThDPs in the two active sites of the E1 (EC 1.2.4.1) component of the pyruvate dehydrogenase complex communicate over a distance of 20 angst ...

    Thiamine diphosphate (ThDP) is used as a cofactor in many key metabolic enzymes. We present evidence that the ThDPs in the two active sites of the E1 (EC 1.2.4.1) component of the pyruvate dehydrogenase complex communicate over a distance of 20 angstroms by reversibly shuttling a proton through an acidic tunnel in the protein. This "proton wire" permits the co-factors to serve reciprocally as general acid/base in catalysis and to switch the conformation of crucial active-site peptide loops. This synchronizes the progression of chemical events and can account for the oligomeric organization, conformational asymmetry, and "ping-pong" kinetic properties of E1 and other thiamine-dependent enzymes.


    Related Citations: 
    • Molecular Assembly of a Multi-Enzymes Complex: The Crystal Structure of Pyruvate Dehydrogenase E1 Bound to the Peripheral Subunit Binding Domain of E2
      Frank, R.A.W., Pratap, J.V., Pei, X.Y., Perham, R.N., Luisi, B.F.
      () To be published --: --

    Organizational Affiliation

    Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNITBDFH324Geobacillus stearothermophilusMutation(s): 0 
Gene Names: pdhB
EC: 1.2.4.1
Find proteins for P21874 (Geobacillus stearothermophilus)
Explore P21874 
Go to UniProtKB:  P21874
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNITACEG368Geobacillus stearothermophilusMutation(s): 0 
Gene Names: pdhA
EC: 1.2.4.1
Find proteins for P21873 (Geobacillus stearothermophilus)
Explore P21873 
Go to UniProtKB:  P21873
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATEIJ49Geobacillus stearothermophilusMutation(s): 0 
Gene Names: pdhC
EC: 2.3.1.12
Find proteins for P11961 (Geobacillus stearothermophilus)
Explore P11961 
Go to UniProtKB:  P11961
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TDP
Query on TDP

Download CCD File 
A, C, E, G
THIAMIN DIPHOSPHATE
C12 H18 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download CCD File 
A, C, G
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
B, D, F, H
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C, E, F, G
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.27α = 90
b = 232.33β = 90.81
c = 91.924γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-02
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-05-08
    Changes: Atomic model, Data collection, Database references, Experimental preparation, Other